SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 17 of 17
Search took 0.00 seconds.
Search: Posts Made By: greener
Forum: Bioinformatics 08-30-2013, 03:06 PM
Replies: 2
Views: 2,334
Posted By greener
Different normalization methods with count data

Hello folks, Quick question. I have RNAseq count data sets which I would like to analyze together. Experimentall they are similair they only differ by their depths of coverage . One set has about 30...
Forum: Bioinformatics 12-27-2012, 04:45 PM
Replies: 1
Views: 2,072
Posted By greener
generation of GTF file from a gbff?

Howdy folks, quick question .I recently pulled down some cyno genome data that included a fasta, asn, and gbff file. I create an index with bowtie2 from the fasta and ran it with no problems. I would...
Forum: Bioinformatics 04-24-2012, 12:30 PM
Replies: 14
Views: 3,637
Posted By greener
here is one [greener@kojak bowtie]$ head -n...

here is one

[greener@kojak bowtie]$ head -n 10 /vol01/genome/mouse/ucsc/annotation/mm9_ucsc_refGene.txt.gtf2.2
chr1 ucsc exon 134212701 134213049 . + 0 ...
Forum: Bioinformatics 04-23-2012, 08:35 AM
Replies: 14
Views: 3,637
Posted By greener
Thanks areyes, Yes I did try it with an out file....

Thanks areyes, Yes I did try it with an out file. still get the same error
Forum: Bioinformatics 04-20-2012, 06:49 AM
Replies: 14
Views: 3,637
Posted By greener
errors while using python dexseq_prepare_annotation.py

Hi there, I am trying to use the dexseq_prepare_annotation.py tool in DEXseq and have tried several different gtf files but they all seem to get the same error. Not sure what could be causing this...
Forum: Bioinformatics 04-02-2012, 04:15 PM
Replies: 6
Views: 3,370
Posted By greener
PCA with cufflinks data

I was wondering if folks had any advice on the simplest way to generate a principal component analysis or MDS plot with Cufflinks output. I could group all my Cufflinks output into a data matrix and...
Forum: Bioinformatics 02-14-2012, 09:35 AM
Replies: 4
Views: 2,372
Posted By greener
awesome , so you are using SGE with Bowtie? what...

awesome , so you are using SGE with Bowtie? what tools are using with it?
Forum: Bioinformatics 02-13-2012, 02:43 PM
Replies: 4
Views: 2,372
Posted By greener
Best deployment method of NGS tools on a cluster?

Howdy everyone,
We are building a small rocks cluster (4-5 nodes to start) and I am hoping to configure it to perform some denovo tools (abyss and trinity) but also to be able to run the tuxedo...
Forum: General 10-10-2011, 12:49 PM
Replies: 0
Views: 1,233
Posted By greener
methods journals: NGS

Can anyone recommend any methods journals that have published NGS papers? Thanks -Rich
Forum: Bioinformatics 05-02-2011, 05:52 AM
Replies: 16
Views: 5,242
Posted By greener
Cool

I am definitely interested in your scripts as well. We would definitely try them with our RNAseq data. Could you please
Send them to greener@u.washington.edu
Thanks!
-Rich
Forum: Bioinformatics 04-29-2011, 11:52 AM
Replies: 1
Views: 2,626
Posted By greener
Public repositories for NGS data

Hello again, Now that the NIH's public repository for NGS data is shutting down what alternative sites are folks using to upload their NGS results?
Thanks
-Rich
Forum: Bioinformatics 04-29-2011, 11:51 AM
Replies: 0
Views: 994
Posted By greener
Looking for advice on known non-coding annotation:

Howdy folks, I wanted to get some suggestions from people on the best, most update, most detailed sources of known non-coding annotation. If I grep out the NRs from the refseq , I can get a limited...
Forum: RNA Sequencing 04-14-2011, 08:08 PM
Replies: 5
Views: 6,116
Posted By greener
Is more than two conditions possible in DESEQ?

Going through the literature , it doesn't seem that you can provide more than two conditions for the negative binomial distribution. If someone knows a way to provide more than one I'd be very...
Forum: Bioinformatics 03-08-2011, 03:49 PM
Replies: 11
Views: 7,016
Posted By greener
Hi Rachelly, I seem to having the same problem....

Hi Rachelly, I seem to having the same problem. My Cuffdiff output does not contain gene names. Could you post an example of a reference file that worked and the commands you ran that worked? I tried...
Forum: Bioinformatics 02-25-2011, 02:37 PM
Replies: 0
Views: 1,929
Posted By greener
Does Cuffdiff normalize FPKMS before it does differential expression?

Does Cuffdiff normalize FPKMs before it runs differential expression? If so what kind of normalization is performed? Can't find it in the documentation. Any ideas folks have are appreciated. Thanks...
Forum: Bioinformatics 02-23-2011, 06:45 AM
Replies: 3
Views: 2,999
Posted By greener
Thanks Reut, It was my understanding that one's...

Thanks Reut, It was my understanding that one's individual cufflinks run generate normalized FPKMs. I have run multiple cufflinks runs across conditions, time points, and with replicates. I'm curious...
Forum: Bioinformatics 02-22-2011, 02:47 PM
Replies: 3
Views: 2,999
Posted By greener
Normalization of FPKMs from Cufflinks

Hi there,
I have been using the Tuxedo suite tools , specifically I have been using bowtie, tophat,and cufflinks. Now that I have FPKM values I have a couple of questions.
1. What are the most...
Showing results 1 to 17 of 17

 


All times are GMT -8. The time now is 04:46 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO